Universitat Internacional de Catalunya

Biomolecular Interaction

Biomolecular Interaction
3
13504
3
Second semester
OB
BASIC HEALTH INFORMATICS TOOLS
Main language of instruction: Spanish

Other languages of instruction: Catalan, English

Teaching staff


Dr. VIAYNA GAZA, Antonio - aviayna@uic.es

Students can request an appointment with the lecturer by email:

Antonio Viayna: aviayna@uic.es

 

Introduction

All biological system is formed by a large and diverse network of biomolecular interactions. In this course, the student will understand how biomolecules interact, what experimental techniques and in silico tools are available for the analysis of protein-protein and protein-ligand interactions. The student will become familiar with databases and will use available databases and servers to study and analyze biomolecule interactions. They will be introduced in the state-of-the-art of structural bioinformatics for the in-silico simulation and prediction of biomolecular interactions.

 

Pre-course requirements

Structural and functional knowledge of molecules, genetics, cellular biology, and molecular biology.

Objectives

  • To know the energetic mechanisms involved in biomolecular interactions.
  • To learn and to extract information from databases and servers.
  • To know the experimental techniques used for the study and structural characterization of biomolecular interactions.
  • To understand and to run bioinformatic tools for the molecular simulation and prediction of biomolecule interactions.

Competences/Learning outcomes of the degree programme

Basic competencies:

- That students have demonstrated knowledge and understanding in a field of study that part of the basis of general secondary education, and is typically at a level which, although it is supported by advanced textbooks, includes some aspects that will knowledge of the forefront of their field of study.

- That students have the ability to gather and interpret relevant data (usually within their field of study) to inform judgments that include reflection on relevant social, scientific or ethical.


General and specific competencies:

- To use bioinformatic tools typical for the area of biomedical research.

- To identify and to know to use the elemental tools typical for the bioinformatics field and to get to analyze the structure and interaction of principal biomolecules.


 Transversal competencies:

- To develop the capacity of organization and planning appropriate to the moment.
- To develop the ability to solve problems.
- To develop the capacity of analysis and synthesis.
- Interpret experimental results and identify consistent and inconsistent elements.
- To use the Internet as a medium of communication and as a source of information.
- To know how to communicate, make presentations and write scientific papers.
- To be able to teamwork.
- To reason and evaluate situations and results from a critical and constructive point of view.
- To have the ability to develop skills in interpersonal relationships.
- To be able to carry out autonomous learning.
- To apply theoretical knowledge to practice.
- To apply the scientific method.
- To respect the fundamental rights of equality between men and women, and the promotion of human rights and the values of a culture of peace and democratic values.

 

Learning outcomes of the subject

  • Knows how to use the most used databases to predict and extract information of interaction of biomolecules.
  • Uses bioinformatic tools to characterize and predict the interaction of biomolecules at the structural level.
  • Knows the current limitations of molecular interactions research.
  • Works in team, reasoning and applying the scientific method.

Syllabus

Master classes (CM):

  1. Fundamentals of biomolecular interactions
    1. Physicochemical properties
    2. Types of protein interactions
      • Protein-protein
      • Protein-ligand
    3. Genetic variants in health and disease
    4. Impact of mutations on protein structure and function
  2. Prominent databases of biomolecular interactions
    1. Protein-protein/ligand complexes
    2. Protein-protein networks
    3. Disease-related networks
    4. Molecular and metabolic pathway networks
    5. Binding affinity
  3. Characterization of protein interactions
    1. Structural characterization of protein interactions
      1. Experimental techniques
      2. Computational characterization of protein and protein-protein/ligand interfaces
      3. Computational modeling of protein interactions
        • Template-based docking
        • Ab initio docking
      4. Integrative modeling of protein interactions
    2. Energetic characterization of protein interactions
      1. Experimental techniques
      2. Computational tools available
    3. Current limitations

Case Methods (MC):

  1. Analysis of specific protein-protein interaction using interaction databases.
  2. Protein-ligand simulation.
  3. Prediction of binding energy changes upon mutation.

Laboratory:

  1. Databases and servers for the structural characterization of proteins and biomolecular interactions.
  2. Use of computational tools for the simulation and prediction of molecular interactions related with Malaria.

Teaching and learning activities

In person



Master classes: Theorical lesson in two sessions of 50min. oral presentation given by the lecturer.

Case Methods (MC): Approach to a real or imaginary situation. Students work on the questions formulated in small groups or in active interaction with the teacher and the answers are discussed. The teacher actively takes part and provides new knowledge.

Practical sessions: These are performed in reduced groups. The teacher proposes a problem and intercede searching the solution, the students develop the implemented methodology performed by the teacher.

Virtual education (EV): On-line material is available by the intranet.

Evaluation systems and criteria

In person



1)    Students in the first call:  

Partial exam 20%
Final exam: 40%
Case Methods: 20%
Practical sessions: 20%

2)    Students in the second chance:

Only there is chance to repeat the final exam. Computing in the final grade the partial exam, methods of the case and the practical exercises obtained in the first call.

3)    Students who repeat the subject: 

The continuous assessment grade (participation in class, case methods, practical sessions) will be saved, although whenever they wish, students can repeat the class assistance and obtain a new grade. On the other hand, students will be able to choose whether to do the partial and the final, or if they do only the final, which will count 60% of the grade.

General points to bearing in mind about the evaluation system:  

1) To pass the course the student must obtain a minimum grade of 5 in the final exam to get a mean of all grades.

2) The exams will be single-shoice test. The multi-choice test has 4 answer options, count +1 each answer and -0.25 each incorrect answer.

3) Class attendance:

  • The regular attendance is recommended for the theorical sessions.
  • Attending at master classes is not mandatory, but attendees will have to abide by the rules indicated by the teachers. The expulsion of a student from the master class or the case method will negatively affect the continuous evaluations.
  • The attendance to the case methods is mandatory. All case methods will be evaluated. The lack of attendance must be justified (illness, vaccine citation, etc.), on the contrary, the right to be evaluated by the method of the specific case will be lost.
  • The attendance to the practical sessions is mandatory and the student must attend in assigned groups. The expulsion of a student from the practice room will mean the automatic suspension of the subject.  

4) When granting Honours, special consideration will be given to the candidates for their participation and involvement in the subject, as well as respect for the basic rules.

5) The inappropriate use of electronic devices such as mobile phones, tablets or laptops can lead to expulsion from class. Inappropriate use is understood as the recording and dissemination of both students and teachers during the different lessons, as well as the use of these devices for recreational and non-educational purposes.

Bibliography and resources

Protein Structure Prediction. Methods in Molecular Biology, vol 2165 (2020). Humana Press. Edited by Daisuke Kihara. ISBN: 978-1-0716-0710-7. https://link.springer.com/book/10.1007/978-1-0716-0708-4

Protein-Protein Interactions. Methods in Molecular Biology, vol 1278 (2015). Human Press. Edited by Cheryl L. Meyerkord, Haian Fu. ISBN: 978-1-4939-2425-7. https://link.springer.com/book/10.1007/978-1-4939-2425-7

Protein-Protein Interactions and Networks. Methods in Molecular Biology, vol (2008). Humana Press. Edited by Panchenko A, Przytycka T. ISBN: 978-1-84800-125-1 https://link.springer.com/book/10.1007/978-1-84800-125-1

Protein-Ligand Interactions. Methods in Molecular Biology, vol 305 (2005). Humana Press. Edited by G. Ulrich Nienhaus. ISBN: 978-1-61737-525-5. https://link.springer.com/book/10.1385/1592599125

Protein-Protein Interactions in Human Disease. Advances in Protein Chemistry and Structural Biology, vol 110 (2018). Edited by Rossen Donev. ISBN: 978-0-12-814344-5. https://www.sciencedirect.com/bookseries/advances-in-protein-chemistry-and-structural-biology/vol/110/suppl/C

Structural Bioinformatics. Methods in Molecular Biology, vol 2112 (2020). Humana Press. Edited by Zoltán Gáspári. ISBN: 978-1-0716-0272-0. https://link.springer.com/book/10.1007/978-1-0716-0270-6

Lehninger: principles of biochemistry (4th edn) D. L. Nelson and M. C. Cox, W. H. Freeman & Co., New York ISBN 0-7167-4339-6 (2004). https://onlinelibrary.wiley.com/doi/10.1002/cbf.1216

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, et al. (2021), Proteins, 89(12):1800-1823. https://doi.org/10.1002/prot.26222

Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. Navío D, Rosell M, Aguirre J, de la Cruz X, Fernández-Recio J. (2019), Int J Mol Sci, 20(7):1583. https://doi.org/10.3390/ijms20071583

Hot-spot analysis for drug discovery targeting protein-protein interactions. Expert Opin Drug Discov. Rosell M, Fernández-Recio J. (2018), 13(4):327-338. https://doi.org/10.1080/17460441.2018.1430763

Weak protein–ligand interactions studied by small-angle X-ray scattering. Tuukkanen, A.T. and Svergun, D.I. (2014), FEBS J, 281: 1974-1987. https://doi.org/10.1111/febs.12772

First homology model of Plasmodium falciparum glucose-6-phosphate dehydrogenase: Discovery of selective substrate analog-based inhibitors as novel antimalarial agents. Alencar N, Sola I, Linares M, Juárez-Jiménez J, Pont C, Viayna A, Vílchez D, et al. (2018), Eur J Med Chem, 146:108-122. https://doi.org/10.1016/j.ejmech.2018.01.044

Docking-based identification of small-molecule binding sites at protein-protein interfaces. Rosell M, Fernández-Recio J. (2020), Comput Struct Biotechnol J., 18:3750-3761. https://doi.org/10.1016/j.csbj.2020.11.029

 

 

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